TY  - JOUR
AU  - Wallace, Megan A
AU  - Coffman, Kelsey A
AU  - Gilbert, Clément
AU  - Ravindran, Sanjana
AU  - Albery, Gregory F
AU  - Abbott, Jessica
AU  - Argyridou, Eliza
AU  - Bellosta, Paola
AU  - Betancourt, Andrea J
AU  - Colinet, Hervé
AU  - Eric, Katarina
AU  - Glaser-Schmitt, Amanda
AU  - Grath, Sonja
AU  - Jelić, Mihailo
AU  - Kankare, Maaria
AU  - Kozeretska, Iryna
AU  - Loeschcke, Volker
AU  - Montchamp-Moreau, Catherine
AU  - Ometto, Lino
AU  - Onder, Banu Sebnem
AU  - Orengo, Dorcas J
AU  - Parsch, John
AU  - Pascual, Marta
AU  - Patenković, Aleksandra
AU  - Puerma, Eva
AU  - Ritchie, Michael G
AU  - Rota-Stabelli, Omar
AU  - Schou, Mads Fristrup
AU  - Serga, Svitlana V
AU  - Stamenković-Radak, Marina
AU  - Tanasković, Marija
AU  - Savić Veselinović, Marija
AU  - Vieira, Jorge
AU  - Vieira, Cristina P
AU  - Kapun, Martin
AU  - Flatt, Thomas
AU  - González, Josefa
AU  - Staubach, Fabian
AU  - Obbard, Darren J
PY  - 2021
UR  - https://academic.oup.com/ve/advance-article/doi/10.1093/ve/veab031/6207981
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4184
AB  - Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here we report fourteen DNA viruses detected in a metagenomic analysis of approximately 6500 pool-sequenced Drosophila, sampled from 47 European locations between 2014 and 2016. These include three new nudiviruses, a new and divergent entomopoxvirus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of galbut virus, a dsRNA partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a bidnavirus, may be composed of up to 12 segments and thus represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2% or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly-available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D. melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.
T2  - Virus Evolution
T2  - Virus Evolution
T1  - The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe
DO  - 10.1093/ve/veab031
ER  - 

@article{
author = "Wallace, Megan A and Coffman, Kelsey A and Gilbert, Clément and Ravindran, Sanjana and Albery, Gregory F and Abbott, Jessica and Argyridou, Eliza and Bellosta, Paola and Betancourt, Andrea J and Colinet, Hervé and Eric, Katarina and Glaser-Schmitt, Amanda and Grath, Sonja and Jelić, Mihailo and Kankare, Maaria and Kozeretska, Iryna and Loeschcke, Volker and Montchamp-Moreau, Catherine and Ometto, Lino and Onder, Banu Sebnem and Orengo, Dorcas J and Parsch, John and Pascual, Marta and Patenković, Aleksandra and Puerma, Eva and Ritchie, Michael G and Rota-Stabelli, Omar and Schou, Mads Fristrup and Serga, Svitlana V and Stamenković-Radak, Marina and Tanasković, Marija and Savić Veselinović, Marija and Vieira, Jorge and Vieira, Cristina P and Kapun, Martin and Flatt, Thomas and González, Josefa and Staubach, Fabian and Obbard, Darren J",
year = "2021",
abstract = "Drosophila melanogaster is an important model for antiviral immunity in arthropods, but very few DNA viruses have been described from the family Drosophilidae. This deficiency limits our opportunity to use natural host-pathogen combinations in experimental studies, and may bias our understanding of the Drosophila virome. Here we report fourteen DNA viruses detected in a metagenomic analysis of approximately 6500 pool-sequenced Drosophila, sampled from 47 European locations between 2014 and 2016. These include three new nudiviruses, a new and divergent entomopoxvirus, a virus related to Leptopilina boulardi filamentous virus, and a virus related to Musca domestica salivary gland hypertrophy virus. We also find an endogenous genomic copy of galbut virus, a dsRNA partitivirus, segregating at very low frequency. Remarkably, we find that Drosophila Vesanto virus, a small DNA virus previously described as a bidnavirus, may be composed of up to 12 segments and thus represent a new lineage of segmented DNA viruses. Two of the DNA viruses, Drosophila Kallithea nudivirus and Drosophila Vesanto virus are relatively common, found in 2% or more of wild flies. The others are rare, with many likely to be represented by a single infected fly. We find that virus prevalence in Europe reflects the prevalence seen in publicly-available datasets, with Drosophila Kallithea nudivirus and Drosophila Vesanto virus the only ones commonly detectable in public data from wild-caught flies and large population cages, and the other viruses being rare or absent. These analyses suggest that DNA viruses are at lower prevalence than RNA viruses in D. melanogaster, and may be less likely to persist in laboratory cultures. Our findings go some way to redressing an earlier bias toward RNA virus studies in Drosophila, and lay the foundation needed to harness the power of Drosophila as a model system for the study of DNA viruses.",
journal = "Virus Evolution, Virus Evolution",
title = "The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe",
doi = "10.1093/ve/veab031"
}

Wallace, M. A., Coffman, K. A., Gilbert, C., Ravindran, S., Albery, G. F., Abbott, J., Argyridou, E., Bellosta, P., Betancourt, A. J., Colinet, H., Eric, K., Glaser-Schmitt, A., Grath, S., Jelić, M., Kankare, M., Kozeretska, I., Loeschcke, V., Montchamp-Moreau, C., Ometto, L., Onder, B. S., Orengo, D. J., Parsch, J., Pascual, M., Patenković, A., Puerma, E., Ritchie, M. G., Rota-Stabelli, O., Schou, M. F., Serga, S. V., Stamenković-Radak, M., Tanasković, M., Savić Veselinović, M., Vieira, J., Vieira, C. P., Kapun, M., Flatt, T., González, J., Staubach, F.,& Obbard, D. J.. (2021). The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe. in Virus Evolution.
https://doi.org/10.1093/ve/veab031

Wallace MA, Coffman KA, Gilbert C, Ravindran S, Albery GF, Abbott J, Argyridou E, Bellosta P, Betancourt AJ, Colinet H, Eric K, Glaser-Schmitt A, Grath S, Jelić M, Kankare M, Kozeretska I, Loeschcke V, Montchamp-Moreau C, Ometto L, Onder BS, Orengo DJ, Parsch J, Pascual M, Patenković A, Puerma E, Ritchie MG, Rota-Stabelli O, Schou MF, Serga SV, Stamenković-Radak M, Tanasković M, Savić Veselinović M, Vieira J, Vieira CP, Kapun M, Flatt T, González J, Staubach F, Obbard DJ. The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe. in Virus Evolution. 2021;.
doi:10.1093/ve/veab031 .

Wallace, Megan A, Coffman, Kelsey A, Gilbert, Clément, Ravindran, Sanjana, Albery, Gregory F, Abbott, Jessica, Argyridou, Eliza, Bellosta, Paola, Betancourt, Andrea J, Colinet, Hervé, Eric, Katarina, Glaser-Schmitt, Amanda, Grath, Sonja, Jelić, Mihailo, Kankare, Maaria, Kozeretska, Iryna, Loeschcke, Volker, Montchamp-Moreau, Catherine, Ometto, Lino, Onder, Banu Sebnem, Orengo, Dorcas J, Parsch, John, Pascual, Marta, Patenković, Aleksandra, Puerma, Eva, Ritchie, Michael G, Rota-Stabelli, Omar, Schou, Mads Fristrup, Serga, Svitlana V, Stamenković-Radak, Marina, Tanasković, Marija, Savić Veselinović, Marija, Vieira, Jorge, Vieira, Cristina P, Kapun, Martin, Flatt, Thomas, González, Josefa, Staubach, Fabian, Obbard, Darren J, "The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe" in Virus Evolution (2021),
https://doi.org/10.1093/ve/veab031 . .

TY  - JOUR
AU  - Kapun, Martin
AU  - Nunez, Joaquin C B
AU  - Bogaerts-Márquez, María
AU  - Murga-Moreno, Jesús
AU  - Paris, Margot
AU  - Outten, Joseph
AU  - Coronado-Zamora, Marta
AU  - Tern, Courtney
AU  - Rota-Stabelli, Omar
AU  - Guerreiro, Maria P García
AU  - Casillas, Sònia
AU  - Orengo, Dorcas J
AU  - Puerma, Eva
AU  - Kankare, Maaria
AU  - Ometto, Lino
AU  - Loeschcke, Volker
AU  - Onder, Banu S
AU  - Abbott, Jessica K
AU  - Schaeffer, Stephen W
AU  - Rajpurohit, Subhash
AU  - Behrman, Emily L
AU  - Schou, Mads F
AU  - Merritt, Thomas J S
AU  - Lazzaro, Brian P
AU  - Glaser-Schmitt, Amanda
AU  - Argyridou, Eliza
AU  - Staubach, Fabian
AU  - Wang, Yun
AU  - Tauber, Eran
AU  - Serga, Svitlana V
AU  - Fabian, Daniel K
AU  - Dyer, Kelly A
AU  - Wheat, Christopher W
AU  - Parsch, John
AU  - Grath, Sonja
AU  - Savić Veselinović, Marija
AU  - Stamenković-Radak, Marina
AU  - Jelić, Mihailo
AU  - Buendía-Ruíz, Antonio J
AU  - Gómez-Julián, Maria Josefa
AU  - Espinosa-Jimenez, Maria Luisa
AU  - Gallardo-Jiménez, Francisco D
AU  - Patenković, Aleksandra
AU  - Erić, Katarina
AU  - Tanasković, Marija
AU  - Ullastres, Anna
AU  - Guio, Lain
AU  - Merenciano, Miriam
AU  - Guirao-Rico, Sara
AU  - Horváth, Vivien
AU  - Obbard, Darren J
AU  - Pasyukova, Elena
AU  - Alatortsev, Vladimir E
AU  - Vieira, Cristina P
AU  - Vieira, Jorge
AU  - Torres, Jorge Roberto
AU  - Kozeretska, Iryna
AU  - Maistrenko, Oleksandr M
AU  - Montchamp-Moreau, Catherine
AU  - Mukha, Dmitry V
AU  - Machado, Heather E
AU  - Lamb, Keric
AU  - Paulo, Tânia
AU  - Yusuf, Leeban
AU  - Barbadilla, Antonio
AU  - Petrov, Dmitri
AU  - Schmidt, Paul
AU  - Gonzalez, Josefa
AU  - Flatt, Thomas
AU  - Bergland, Alan O
AU  - Nielsen, Rasmus
PY  - 2021
UR  - https://academic.oup.com/mbe/article/38/12/5782/6361628
UR  - http://radar.ibiss.bg.ac.rs/handle/123456789/4765
AB  - Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.
PB  - Oxford: Oxford University Press
T2  - Molecular Biology and Evolution
T1  - Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource
IS  - 12
VL  - 38
DO  - 10.1093/molbev/msab259
SP  - 5782
EP  - 5805
ER  - 

@article{
author = "Kapun, Martin and Nunez, Joaquin C B and Bogaerts-Márquez, María and Murga-Moreno, Jesús and Paris, Margot and Outten, Joseph and Coronado-Zamora, Marta and Tern, Courtney and Rota-Stabelli, Omar and Guerreiro, Maria P García and Casillas, Sònia and Orengo, Dorcas J and Puerma, Eva and Kankare, Maaria and Ometto, Lino and Loeschcke, Volker and Onder, Banu S and Abbott, Jessica K and Schaeffer, Stephen W and Rajpurohit, Subhash and Behrman, Emily L and Schou, Mads F and Merritt, Thomas J S and Lazzaro, Brian P and Glaser-Schmitt, Amanda and Argyridou, Eliza and Staubach, Fabian and Wang, Yun and Tauber, Eran and Serga, Svitlana V and Fabian, Daniel K and Dyer, Kelly A and Wheat, Christopher W and Parsch, John and Grath, Sonja and Savić Veselinović, Marija and Stamenković-Radak, Marina and Jelić, Mihailo and Buendía-Ruíz, Antonio J and Gómez-Julián, Maria Josefa and Espinosa-Jimenez, Maria Luisa and Gallardo-Jiménez, Francisco D and Patenković, Aleksandra and Erić, Katarina and Tanasković, Marija and Ullastres, Anna and Guio, Lain and Merenciano, Miriam and Guirao-Rico, Sara and Horváth, Vivien and Obbard, Darren J and Pasyukova, Elena and Alatortsev, Vladimir E and Vieira, Cristina P and Vieira, Jorge and Torres, Jorge Roberto and Kozeretska, Iryna and Maistrenko, Oleksandr M and Montchamp-Moreau, Catherine and Mukha, Dmitry V and Machado, Heather E and Lamb, Keric and Paulo, Tânia and Yusuf, Leeban and Barbadilla, Antonio and Petrov, Dmitri and Schmidt, Paul and Gonzalez, Josefa and Flatt, Thomas and Bergland, Alan O and Nielsen, Rasmus",
year = "2021",
abstract = "Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.",
publisher = "Oxford: Oxford University Press",
journal = "Molecular Biology and Evolution",
title = "Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource",
number = "12",
volume = "38",
doi = "10.1093/molbev/msab259",
pages = "5782-5805"
}

Kapun, M., Nunez, J. C. B., Bogaerts-Márquez, M., Murga-Moreno, J., Paris, M., Outten, J., Coronado-Zamora, M., Tern, C., Rota-Stabelli, O., Guerreiro, M. P. G., Casillas, S., Orengo, D. J., Puerma, E., Kankare, M., Ometto, L., Loeschcke, V., Onder, B. S., Abbott, J. K., Schaeffer, S. W., Rajpurohit, S., Behrman, E. L., Schou, M. F., Merritt, T. J. S., Lazzaro, B. P., Glaser-Schmitt, A., Argyridou, E., Staubach, F., Wang, Y., Tauber, E., Serga, S. V., Fabian, D. K., Dyer, K. A., Wheat, C. W., Parsch, J., Grath, S., Savić Veselinović, M., Stamenković-Radak, M., Jelić, M., Buendía-Ruíz, A. J., Gómez-Julián, M. J., Espinosa-Jimenez, M. L., Gallardo-Jiménez, F. D., Patenković, A., Erić, K., Tanasković, M., Ullastres, A., Guio, L., Merenciano, M., Guirao-Rico, S., Horváth, V., Obbard, D. J., Pasyukova, E., Alatortsev, V. E., Vieira, C. P., Vieira, J., Torres, J. R., Kozeretska, I., Maistrenko, O. M., Montchamp-Moreau, C., Mukha, D. V., Machado, H. E., Lamb, K., Paulo, T., Yusuf, L., Barbadilla, A., Petrov, D., Schmidt, P., Gonzalez, J., Flatt, T., Bergland, A. O.,& Nielsen, R.. (2021). Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. in Molecular Biology and Evolution
Oxford: Oxford University Press., 38(12), 5782-5805.
https://doi.org/10.1093/molbev/msab259

Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, Guerreiro MPG, Casillas S, Orengo DJ, Puerma E, Kankare M, Ometto L, Loeschcke V, Onder BS, Abbott JK, Schaeffer SW, Rajpurohit S, Behrman EL, Schou MF, Merritt TJS, Lazzaro BP, Glaser-Schmitt A, Argyridou E, Staubach F, Wang Y, Tauber E, Serga SV, Fabian DK, Dyer KA, Wheat CW, Parsch J, Grath S, Savić Veselinović M, Stamenković-Radak M, Jelić M, Buendía-Ruíz AJ, Gómez-Julián MJ, Espinosa-Jimenez ML, Gallardo-Jiménez FD, Patenković A, Erić K, Tanasković M, Ullastres A, Guio L, Merenciano M, Guirao-Rico S, Horváth V, Obbard DJ, Pasyukova E, Alatortsev VE, Vieira CP, Vieira J, Torres JR, Kozeretska I, Maistrenko OM, Montchamp-Moreau C, Mukha DV, Machado HE, Lamb K, Paulo T, Yusuf L, Barbadilla A, Petrov D, Schmidt P, Gonzalez J, Flatt T, Bergland AO, Nielsen R. Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource. in Molecular Biology and Evolution. 2021;38(12):5782-5805.
doi:10.1093/molbev/msab259 .

Kapun, Martin, Nunez, Joaquin C B, Bogaerts-Márquez, María, Murga-Moreno, Jesús, Paris, Margot, Outten, Joseph, Coronado-Zamora, Marta, Tern, Courtney, Rota-Stabelli, Omar, Guerreiro, Maria P García, Casillas, Sònia, Orengo, Dorcas J, Puerma, Eva, Kankare, Maaria, Ometto, Lino, Loeschcke, Volker, Onder, Banu S, Abbott, Jessica K, Schaeffer, Stephen W, Rajpurohit, Subhash, Behrman, Emily L, Schou, Mads F, Merritt, Thomas J S, Lazzaro, Brian P, Glaser-Schmitt, Amanda, Argyridou, Eliza, Staubach, Fabian, Wang, Yun, Tauber, Eran, Serga, Svitlana V, Fabian, Daniel K, Dyer, Kelly A, Wheat, Christopher W, Parsch, John, Grath, Sonja, Savić Veselinović, Marija, Stamenković-Radak, Marina, Jelić, Mihailo, Buendía-Ruíz, Antonio J, Gómez-Julián, Maria Josefa, Espinosa-Jimenez, Maria Luisa, Gallardo-Jiménez, Francisco D, Patenković, Aleksandra, Erić, Katarina, Tanasković, Marija, Ullastres, Anna, Guio, Lain, Merenciano, Miriam, Guirao-Rico, Sara, Horváth, Vivien, Obbard, Darren J, Pasyukova, Elena, Alatortsev, Vladimir E, Vieira, Cristina P, Vieira, Jorge, Torres, Jorge Roberto, Kozeretska, Iryna, Maistrenko, Oleksandr M, Montchamp-Moreau, Catherine, Mukha, Dmitry V, Machado, Heather E, Lamb, Keric, Paulo, Tânia, Yusuf, Leeban, Barbadilla, Antonio, Petrov, Dmitri, Schmidt, Paul, Gonzalez, Josefa, Flatt, Thomas, Bergland, Alan O, Nielsen, Rasmus, "Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource" in Molecular Biology and Evolution, 38, no. 12 (2021):5782-5805,
https://doi.org/10.1093/molbev/msab259 . .